Related papers: Energy-based View of Retrosynthesis

We describe a fully data driven model that learns to perform a retrosynthetic reaction prediction task, which is treated as a sequence-to-sequence mapping problem. The end-to-end trained model has an encoder-decoder architecture that…

Retrosynthesis is a problem to infer reactant compounds to synthesize a given product compound through chemical reactions. Recent studies on retrosynthesis focus on proposing more sophisticated prediction models, but the dataset to feed the…

We propose a new model for making generalizable and diverse retrosynthetic reaction predictions. Given a target compound, the task is to predict the likely chemical reactants to produce the target. This generative task can be framed as a…

A fundamental problem in computational chemistry is to find a set of reactants to synthesize a target molecule, a.k.a. retrosynthesis prediction. Existing state-of-the-art methods rely on matching the target molecule with a large set of…

Retrosynthesis analysis is a critical task in organic chemistry central to many important industries. Previously, various machine learning approaches have achieved promising results on this task by representing output molecules as strings…

Generative models have shown strong generation ability while efficient likelihood estimation is less explored. Energy-based models~(EBMs) define a flexible energy function to parameterize unnormalized densities efficiently but are notorious…

Retrosynthesis prediction aims to infer the reactant molecule based on a given product molecule, which is a fundamental task in chemical synthesis. However, existing models rely on static pattern-matching paradigm, which limits their…

Energy based models (EBMs) are appealing due to their generality and simplicity in likelihood modeling, but have been traditionally difficult to train. We present techniques to scale MCMC based EBM training on continuous neural networks,…

We propose an energy-based model (EBM) of protein conformations that operates at atomic scale. The model is trained solely on crystallized protein data. By contrast, existing approaches for scoring conformations use energy functions that…

Generative Pre-trained Transformer (GPT) architectures are the most popular design for language modeling. Energy-based modeling is a different paradigm that views inference as a dynamical process operating on an energy landscape. We propose…

One of the predominant methods for training world models is autoregressive prediction in the output space of the next element of a sequence. In Natural Language Processing (NLP), this takes the form of Large Language Models (LLMs)…

Energy-Based Models (EBMs) provide a flexible framework for generative modeling, but their training remains theoretically challenging due to the need to approximate normalization constants and efficiently sample from complex, multi-modal…

Energy-based language models (ELMs) parameterize an unnormalized distribution for natural sentences and are radically different from popular autoregressive language models (ALMs). As an important application, ELMs have been successfully…

Energy-Based Models (EBMs) present a flexible and appealing way to represent uncertainty. Despite recent advances, training EBMs on high-dimensional data remains a challenging problem as the state-of-the-art approaches are costly, unstable,…

Energy-based models (EBMs) are generative models that are usually trained via maximum likelihood estimation. This approach becomes challenging in generic situations where the trained energy is non-convex, due to the need to sample the Gibbs…

Deep generative models have emerged as a popular machine learning-based approach for inverse design problems in the life sciences. However, these problems often require sampling new designs that satisfy multiple properties of interest in…

We present an extension of our Molecular Transformer architecture combined with a hyper-graph exploration strategy for automatic retrosynthesis route planning without human intervention. The single-step retrosynthetic model sets a new state…

Chemical synthesis remains a critical bottleneck in the discovery and manufacture of functional small molecules. AI-based synthesis planning models could be a potential remedy to find effective syntheses, and have made progress in recent…

Learning energy-based model (EBM) requires MCMC sampling of the learned model as an inner loop of the learning algorithm. However, MCMC sampling of EBMs in high-dimensional data space is generally not mixing, because the energy function,…

Retrosynthesis is a major task for drug discovery. It is formulated as a graph-generating problem by many existing approaches. Specifically, these methods firstly identify the reaction center, and break target molecule accordingly to…